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load dataset

ctrl_filtered <- readRDS("./processed_data_file/ctrl_filtered.rds")
HSD_filtered <- readRDS("./processed_data_file/HSD_filtered.rds")

umapplot(ctrl_filtered, group.by = "ref_celltype")

Scale for 'colour' is already present. Adding another scale for 'colour', which will
replace the existing scale.

umapplot(HSD_filtered, group.by = "ref_celltype")

Scale for 'colour' is already present. Adding another scale for 'colour', which will
replace the existing scale.

scmap

ref_sce <- mkref_scmap_from_seuobj(ctrl_filtered)

Parameter M was not provided, will use M = n_features / 10 (if n_features <= 1000), where n_features is the number of selected features, and M = 100 otherwise.
Parameter k was not provided, will use k = sqrt(number_of_cells)

HSD_filtered <- query_scmap_from_refsce(HSD_filtered, ref_sce, ref_labels = 'celltype')

Parameter M was not provided, will use M = n_features / 10 (if n_features <= 1000), where n_features is the number of selected features, and M = 100 otherwise.
Parameter k was not provided, will use k = sqrt(number_of_cells)

umapplot(HSD_filtered,group.by = "scmap_idents")

Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the
existing scale.

prop_confuse_mat

     
               ASP           DB           DT           SB           PC           TC           VB
  ASP 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
  DB  0.0000000000 0.9623103279 0.0110732538 0.0000000000 0.0320699708 0.0000000000 0.0163487738
  DT  0.0000000000 0.0063631914 0.9514480409 0.0064516129 0.0029154519 0.0000000000 0.0000000000
  SB  0.0000000000 0.0004894763 0.0144804089 0.9935483871 0.0029154519 0.0370370370 0.0000000000
  PC  0.0000000000 0.0181106216 0.0000000000 0.0000000000 0.9620991254 0.0000000000 0.0000000000
  TC  0.0000000000 0.0000000000 0.0212947189 0.0000000000 0.0000000000 0.9629629630 0.0000000000
  VB  0.0000000000 0.0073421439 0.0008517888 0.0000000000 0.0000000000 0.0000000000 0.9700272480
  LT  0.0000000000 0.0053842389 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0136239782
  GB  0.0000000000 0.0000000000 0.0008517888 0.0000000000 0.0000000000 0.0000000000 0.0000000000
     
                LT           GB
  ASP 0.0000000000 0.0000000000
  DB  0.0000000000 0.0000000000
  DT  0.0092592593 0.0000000000
  SB  0.0000000000 0.0000000000
  PC  0.0000000000 0.0000000000
  TC  0.0000000000 0.0000000000
  VB  0.0000000000 0.0000000000
  LT  0.9907407407 0.0000000000
  GB  0.0000000000 1.0000000000

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